CONFLIST LYS        LYSBK LYS01 LYS+1

NATOM    LYSBK      6
NATOM    LYS01      15
NATOM    LYS+1      16

IATOM    LYSBK  N   0
IATOM    LYSBK  H   1
IATOM    LYSBK  CA  2
IATOM    LYSBK  HA  3
IATOM    LYSBK  C   4
IATOM    LYSBK  O   5
IATOM    LYS01  CB  0
IATOM    LYS01 1HB  1
IATOM    LYS01 2HB  2
IATOM    LYS01  CG  3
IATOM    LYS01 1HG  4
IATOM    LYS01 2HG  5
IATOM    LYS01  CD  6
IATOM    LYS01 1HD  7
IATOM    LYS01 2HD  8
IATOM    LYS01  CE  9
IATOM    LYS01 1HE  10
IATOM    LYS01 2HE  11
IATOM    LYS01  NZ  12
IATOM    LYS01 1HZ  13
IATOM    LYS01 2HZ  14
IATOM    LYS+1  CB  0
IATOM    LYS+1 1HB  1
IATOM    LYS+1 2HB  2
IATOM    LYS+1  CG  3
IATOM    LYS+1 1HG  4
IATOM    LYS+1 2HG  5
IATOM    LYS+1  CD  6
IATOM    LYS+1 1HD  7
IATOM    LYS+1 2HD  8
IATOM    LYS+1  CE  9
IATOM    LYS+1 1HE  10
IATOM    LYS+1 2HE  11
IATOM    LYS+1  NZ  12
IATOM    LYS+1 1HZ  13
IATOM    LYS+1 2HZ  14
IATOM    LYS+1 3HZ  15

ATOMNAME LYSBK    0  N  
ATOMNAME LYSBK    1  H
ATOMNAME LYSBK    2  CA 
ATOMNAME LYSBK    3  HA 
ATOMNAME LYSBK    4  C  
ATOMNAME LYSBK    5  O  
ATOMNAME LYS01    0  CB 
ATOMNAME LYS01    1 1HB 
ATOMNAME LYS01    2 2HB 
ATOMNAME LYS01    3  CG 
ATOMNAME LYS01    4 1HG
ATOMNAME LYS01    5 2HG 
ATOMNAME LYS01    6  CD 
ATOMNAME LYS01    7 1HD 
ATOMNAME LYS01    8 2HD 
ATOMNAME LYS01    9  CE 
ATOMNAME LYS01   10 1HE 
ATOMNAME LYS01   11 2HE 
ATOMNAME LYS01   12  NZ 
ATOMNAME LYS01   13 1HZ 
ATOMNAME LYS01   14 2HZ 
ATOMNAME LYS+1    0  CB 
ATOMNAME LYS+1    1 1HB 
ATOMNAME LYS+1    2 2HB 
ATOMNAME LYS+1    3  CG 
ATOMNAME LYS+1    4 1HG 
ATOMNAME LYS+1    5 2HG 
ATOMNAME LYS+1    6  CD 
ATOMNAME LYS+1    7 1HD 
ATOMNAME LYS+1    8 2HD 
ATOMNAME LYS+1    9  CE 
ATOMNAME LYS+1   10 1HE 
ATOMNAME LYS+1   11 2HE 
ATOMNAME LYS+1   12  NZ 
ATOMNAME LYS+1   13 1HZ 
ATOMNAME LYS+1   14 2HZ 
ATOMNAME LYS+1   15 3HZ






#1.Basic Conformer Information: name, pka, em, rxn.
PROTON   LYS01      0
PROTON   LYS+1      +1
PKA      LYS01      0.0
PKA      LYS+1      10.4  #lowered from 10.8 during mcce2 benchmark
ELECTRON LYS01      0
ELECTRON LYS+1      0
EM       LYS01      0.0
EM       LYS+1      0.0
#RXN      LYS01      -1.09
#RXN      LYS+1      -18.72
RXN      LYS01      -1.50
RXN      LYS+1      -19.8

#2.Structure Connectivity
#23456789A123456789B123456789C123456789D123456789E123456789F123456789G123456789H123456789I
#23456789A123456789B123456789C123456789D123456789E123456789F123456789G123456789H123456789I
#ONNECT   conf atom  orbital  ires conn ires conn ires conn ires conn
#ONNECT |-----|----|---------|----|----|----|----|----|----|----|----|----|----|----|----|
CONNECT  LYSBK  N   sp2       -1    C   0     CA  0     H
CONNECT  LYSBK  H   s         0     N
CONNECT  LYSBK  CA  sp3       0     N   0     C   0     CB  0     HA
CONNECT  LYSBK  HA  s         0     CA
CONNECT  LYSBK  C   sp2       0     CA  0     O   1     N
CONNECT  LYSBK  O   sp2       0     C
CONNECT  LYS01  CB  sp3       0     CA  0     CG  0    1HB  0    2HB
CONNECT  LYS01 1HB  s         0     CB
CONNECT  LYS01 2HB  s         0     CB
CONNECT  LYS01  CG  sp3       0     CB  0     CD  0    1HG  0    2HG
CONNECT  LYS01 1HG  s         0     CG
CONNECT  LYS01 2HG  s         0     CG
CONNECT  LYS01  CD  sp3       0     CG  0     CE  0    1HD  0    2HD  
CONNECT  LYS01 1HD  s         0     CD
CONNECT  LYS01 2HD  s         0     CD 
CONNECT  LYS01  CE  sp3       0     CD  0     NZ  0    1HE  0    2HE  
CONNECT  LYS01 1HE  s         0     CE
CONNECT  LYS01 2HE  s         0     CE
CONNECT  LYS01  NZ  sp2       0     CE  0    1HZ  0    2HZ 
CONNECT  LYS01 1HZ  s         0     NZ
CONNECT  LYS01 2HZ  s         0     NZ
CONNECT  LYS+1  CB  sp3       0     CA  0     CG  0    1HB  0    2HB
CONNECT  LYS+1 1HB  s         0     CB
CONNECT  LYS+1 2HB  s         0     CB
CONNECT  LYS+1  CG  sp3       0     CB  0     CD  0    1HG  0    2HG
CONNECT  LYS+1 1HG  s         0     CG
CONNECT  LYS+1 2HG  s         0     CG
CONNECT  LYS+1  CD  sp3       0     CG  0     CE  0    1HD  0    2HD
CONNECT  LYS+1 1HD  s         0     CD
CONNECT  LYS+1 2HD  s         0     CD
CONNECT  LYS+1  CE  sp3       0     CD  0     NZ  0    1HE  0    2HE
CONNECT  LYS+1 1HE  s         0     CE
CONNECT  LYS+1 2HE  s         0     CE
CONNECT  LYS+1  NZ  sp3       0     CE  0    1HZ  0    2HZ  0    3HZ
CONNECT  LYS+1 1HZ  s         0     NZ
CONNECT  LYS+1 2HZ  s         0     NZ
CONNECT  LYS+1 3HZ  s         0     NZ
#23456789A123456789B123456789C123456789D123456789E123456789F123456789G123456789H123456789I

#3.Atom Parameters: Partial Charges and Radii
# Radii from "Bondi, J.Phys.Chem., 68, 441, 1964."
RADIUS   LYS    N   1.50
RADIUS   LYS    H   1.00
RADIUS   LYS    CA  2.00
RADIUS   LYS    HA  0.00
RADIUS   LYS    C   1.70
RADIUS   LYS    O   1.40
RADIUS   LYS    CB  2.00
RADIUS   LYS   1HB  0.00
RADIUS   LYS   2HB  0.00
RADIUS   LYS    CG  2.00
RADIUS   LYS   1HG  0.00
RADIUS   LYS   2HG  0.00
RADIUS   LYS    CD  2.00
RADIUS   LYS   1HD  0.00
RADIUS   LYS   2HD  0.00
RADIUS   LYS    CE  2.00
RADIUS   LYS   1HE  0.00
RADIUS   LYS   2HE  0.00
RADIUS   LYS    NZ  1.50
RADIUS   LYS   1HZ  1.00
RADIUS   LYS   2HZ  1.00
RADIUS   LYS   3HZ  1.0

CHARGE   LYSBK  N    -0.350
CHARGE   LYSBK  H     0.250
CHARGE   LYSBK  CA    0.100
CHARGE   LYSBK  C     0.550
CHARGE   LYSBK  O    -0.550
CHARGE   LYS+1  CB    0.000
CHARGE   LYS+1  CD    0.000
CHARGE   LYS+1  CE    0.330
CHARGE   LYS+1  NZ   -0.320
CHARGE   LYS+1 1HZ    0.330
CHARGE   LYS+1 2HZ    0.330
CHARGE   LYS+1 3HZ    0.330
CHARGE   LYS01  CB    0.000
CHARGE   LYS01  CD    0.000
CHARGE   LYS01  CE    0.000
CHARGE   LYS01  NZ   -0.780
CHARGE   LYS01 1HZ    0.390
CHARGE   LYS01 2HZ    0.390

#=========================================================================
#        GRP   #      BOND     AFFECTED_ATOMS
#123456789012345678901234567890
#-------|---|----|-|---------|----|----|----|----|----|----|----|----|----
ROTAMER  LYS   0     CA - CB   CG   CD   CE   NZ
ROTAMER  LYS   1     CB - CG   CD   CE   NZ
ROTAMER  LYS   2     CG - CD   CE   NZ
ROTAMER  LYS   3     CD - CE   NZ
#=========================================================================

